AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yvfB 149 yvfB #2 yveM 258 similar to capsular polysaccharide biosynthesis #3 spsA 300 alternate gene name: ipa-63d Motif number 1 ATAAACAGCACACTGCCGATTAAAATCGACAAACGCA 1 38 0 CACTGCCGAC 0.973283 -112 TAAAATGGTGCAGCGCCGAAGCCCGCCATCAGAAACG 1 80 0 CAGCGCCGGC 0.996254 -70 ATTTTATGCCAACCGCCTTTATATCACCAGTTCCATT 1 111 1 AACCGCCTCC 0.887004 -39 TTGCACCGCCTGAATGGAACTGGTGATATA 1 130 0 CACCGCCTAC 0.99665 -20 CAGCTGCCCACAGCAGAGCCGAGTGCCTCCATTGATA 2 40 0 CAGCAGAGGC 0.789647 -219 GCATCTAAGGCAGCAACTTCAGCTGCCCACAGCAGAG 2 59 0 CAGCAACTGC 0.911962 -200 CACGCCCCGCCAGCGACGACCAGCATCTAAGGCAGCA 2 81 0 CAGCGACGAC 0.989447 -178 AAAAAATCGGCAGCAGCTAAACCGACAATACGTCCTA 2 154 0 CAGCAGCTAA 0.783167 -105 GAGAGACGAAAACCGCCGCAGCTAAACCGATAAAAGA 2 192 1 AACCGCCGAC 0.985911 -67 CGCGATGACTCACCTCCGATGGAAAACGATCTTAGTC 3 53 1 CACCTCCGAC 0.990902 -248 ATAAAAATCGCACCAGCGACTAAGATCGTTTTCCATC 3 70 0 CACCAGCGAC 0.991625 -231 TTCTGAAAAACAGCGGCTGCCCAGAGCGAAATCTGAT 3 163 0 CAGCGGCTAC 0.993345 -138 ATCCTACACCTCCTTCTTGGAACTTCACACCTG 3 278 0 CACCTCCTAC 0.983216 -23 ******** * * Masking position 2 Map Score: 21.4627 Number of sites scoring better than the average of aligned sites = 830 Number in coding regions = 747 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 TTTTTGTAAAGGTGATGTCTCCTGA 2 5 1 TGTAAGGTGA 0.96432 -254 GCTGTGGGCAGCTGAAGTTGCTGCCTTAGAT 2 63 1 GCTAAGTTGC 0.986059 -196 ACGTATTGTCGGTTTAGCTGCTGCCGATTTT 2 158 1 GGTTAGCTGC 0.974513 -101 TTCTTTTATCGGTTTAGCTGCGGCGGTTTTC 2 199 0 GGTTAGCTGC 0.974513 -60 ATGTTCTGGATGTATAGGTGAACGCTCCGCG 3 26 1 TGTTAGGTGA 0.934114 -275 AGCATCAGCCTCATAAGGTGAAAGAGATAAA 3 102 0 TCAAAGGTGA 0.774743 -199 TGTTGCTTATGCTCAAGTTGCGCTAGGGATA 3 230 0 GCTAAGTTGC 0.986037 -71 ACTATCGTTATCTTATGTTGCTTATGCTCAA 3 245 0 TCTATGTTGC 0.896808 -56 TAGTTTCAGGTGTGAAGTTCCAAGAAGGAGG 3 272 1 TGTAAGTTCC 0.908446 -29 *** ******* Masking position 9 Map Score: 7.95099 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 454 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 ATCGACAAACGCACATCTGCCAAAAGCGCT 1 21 0 GCACATCTGC 0.837599 -129 AATAAACAGCACACTGCCGATTAAAATCGA 1 46 0 ACACTGCCGA 0.8403 -104 TTCTGATGGCGGGCTTCGGCGCTGCACCAT 1 83 1 GGGCTTCGGC 0.876628 -67 GCTGCCCACAGCAGAGCCGAGTGCCTCCAT 2 45 0 GCAGAGCCGA 0.974254 -214 GCTCTGCTGTGGGCAGCTGAAGTTGCTGCC 2 58 1 GGGCAGCTGA 0.982446 -201 CCGATTTTTTGGAGAGACGAAAACCGCCGC 2 181 1 GGAGAGACGA 0.869771 -78 TGCTGAAAAAGAACAGCGGACCGATCAGAT 3 140 1 GAACAGCGGA 0.944235 -161 ATTTCGCTCTGGGCAGCCGCTGTTTTTCAG 3 168 1 GGGCAGCCGC 0.993582 -133 ********** Masking position 9 Map Score: 3.98888 Number of sites scoring better than the average of aligned sites = 2172 Number in coding regions = 2042 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 4 CTGCCGATTAAAATCGACAAACGCACATCT 1 33 0 AAATCGACAA 0.972935 -117 GGCAGCAGCTAAACCGACAATACGTCCTAT 2 153 0 AAACCGACAA 0.993093 -106 CGCCGCAGCTAAACCGATAAAAGAATTAGG 2 205 1 AAACCGATAA 0.989137 -54 CTAGGGATACAAACCAATATGCGAAAAGTT 3 209 0 AAACCAATAT 0.90261 -92 ********** Masking position 7 Map Score: 2.11807 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 107 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 AAAATCGACAAACGCACATCTGCCAAAAGC 1 24 0 AACGCACATC 0.97482 -126 CCCCGCCAGCGACGACCAGCATCTAAGGCA 2 84 0 GACGACCAGC 0.978207 -175 AACCCATCCTCACGCCCCGCCAGCGACGAC 2 98 0 CACGCCCCGC 0.991316 -161 TGTATAGGTGAACGCTCCGCGATGACTCAC 3 36 1 AACGCTCCGC 0.986172 -265 GCTCCGCGATGACTCACCTCCGATGGAAAA 3 49 1 GACTCACCTC 0.910487 -252 TTATGCTGAAAAAGAACAGCGGACCGATCA 3 137 1 AAAGAACAGC 0.857008 -164 ********** Masking position 2 Map Score: 2.04751 Number of sites scoring better than the average of aligned sites = 503 Number in coding regions = 455 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 CACACTGCCGATTAAAATCGACAAACGCAC 1 37 0 ATTAAAATCG 0.971734 -113 AGGCGGTTGGCATAAAATGGTGCAGCGCCG 1 99 0 CATAAAATGG 0.913344 -51 TTCGTCTCTCCAAAAAATCGGCAGCAGCTA 2 172 0 CAAAAAATCG 0.962822 -87 CGCACCAGCGACTAAGATCGTTTTCCATCG 3 69 0 ACTAAGATCG 0.928657 -232 GGTGAAAGAGATAAAAATCGCACCAGCGAC 3 87 0 ATAAAAATCG 0.959987 -214 ********** Masking position 5 Map Score: 0.185088 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 299 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 ********** No masking Map Score: 1.17483e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 1.17483e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: 1.17483e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0